In the release notes for beta 4 it mentions "Fixed issue that caused the resource links in the Translation section to not be verse specific."
The footnotes section, however, is still not verse specific. When hovering/clicking a word the footnotes appear for anything from that point onward, to the end of the pericope (it does not cross pericope boundaries, thankfully). This behavior is most problematic when "insert reference text" is selected, especially if the footnotes section is not at the bottom! Choosing not to insert text and keeping the section at the bottom is the current best solution, but this should be addressed before the 29th. I've attached a screencast to demonstrate the current behavior.
http://screencast.com/t/KLVuE3Dr